website/full_javadoc/compbio/metadata/class-use/JobSubmissionException.html

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   7 Uses of Class compbio.metadata.JobSubmissionException\r
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  83 <H2>\r
  84 <B>Uses of Class<br>compbio.metadata.JobSubmissionException</B></H2>\r
  85 </CENTER>\r
  86 \r
  87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
  88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
  89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
  90 Packages that use <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
  91 </TR>\r
  92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  93 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
  94 <TD>&nbsp;&nbsp;</TD>\r
  95 </TR>\r
  96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  97 <TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
  98 <TD>&nbsp;&nbsp;</TD>\r
  99 </TR>\r
 100 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 101 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
 102 <TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
 103 </TR>\r
 104 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 105 <TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
 106 <TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
 107 </TR>\r
 108 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 109 <TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
 110 <TD>An local engine classes responsible for execution of Executables on the local computer
 111  (the same machine as JVM running these classes).&nbsp;</TD>\r
 112 </TR>\r
 113 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 114 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
 115 <TD>A meta-data model for multiple sequence alignment web services
 116  Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
 117 </TR>\r
 118 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 119 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
 120 <TD>&nbsp;&nbsp;</TD>\r
 121 </TR>\r
 122 </TABLE>\r
 123 &nbsp;\r
 124 <P>\r
 125 <A NAME="compbio.data.msa"><!-- --></A>\r
 126 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 127 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 128 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 129 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
 130 </TR>\r
 131 </TABLE>\r
 132 &nbsp;\r
 133 <P>\r
 134 \r
 135 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 136 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 137 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
 138 </TR>\r
 139 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 140 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 141 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 142 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 143 \r
 144 <BR>\r
 145 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
 146 </TR>\r
 147 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 148 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 149 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 150 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 151             java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
 152 \r
 153 <BR>\r
 154 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
 155 </TR>\r
 156 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 157 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 158 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 159 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 160             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&nbsp;preset)</CODE>\r
 161 \r
 162 <BR>\r
 163 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
 164 </TR>\r
 165 </TABLE>\r
 166 &nbsp;\r
 167 <P>\r
 168 <A NAME="compbio.engine"><!-- --></A>\r
 169 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 170 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 171 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 172 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
 173 </TR>\r
 174 </TABLE>\r
 175 &nbsp;\r
 176 <P>\r
 177 \r
 178 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 179 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 180 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
 181 </TR>\r
 182 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 183 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 184 <CODE>static\r
 185 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 186 <TR ALIGN="right" VALIGN="">\r
 187 <TD NOWRAP><FONT SIZE="-1">\r
 188 <CODE>&lt;T&gt; <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
 189 </TR>\r
 190 </TABLE>\r
 191 </CODE></FONT></TD>\r
 192 <TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)">configureExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable)</CODE>\r
 193 \r
 194 <BR>\r
 195 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 196 </TR>\r
 197 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 199 <CODE>static\r
 200 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 201 <TR ALIGN="right" VALIGN="">\r
 202 <TD NOWRAP><FONT SIZE="-1">\r
 203 <CODE>&lt;T&gt; <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
 204 </TR>\r
 205 </TABLE>\r
 206 </CODE></FONT></TD>\r
 207 <TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)">configureExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
 208                     <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
 209 \r
 210 <BR>\r
 211 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 212 </TR>\r
 213 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 214 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 215 <CODE>static\r
 216 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 217 <TR ALIGN="right" VALIGN="">\r
 218 <TD NOWRAP><FONT SIZE="-1">\r
 219 <CODE>&lt;T&gt; <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
 220 </TR>\r
 221 </TABLE>\r
 222 </CODE></FONT></TD>\r
 223 <TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
 224                     java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
 225 \r
 226 <BR>\r
 227 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 228 </TR>\r
 229 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 230 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 231 <CODE>&nbsp;void</CODE></FONT></TD>\r
 232 <TD><CODE><B>SyncExecutor.</B><B><A HREF="../../../compbio/engine/SyncExecutor.html#executeJob()">executeJob</A></B>()</CODE>\r
 233 \r
 234 <BR>\r
 235 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Execute the job</TD>\r
 236 </TR>\r
 237 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 239 <CODE>static&nbsp;<A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
 240 <TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)">getSyncEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
 241 \r
 242 <BR>\r
 243 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 244 </TR>\r
 245 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 246 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 247 <CODE>static&nbsp;<A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
 248 <TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getSyncEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
 249               <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
 250 \r
 251 <BR>\r
 252 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 253 </TR>\r
 254 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 255 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 256 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 257 <TD><CODE><B>AsyncExecutor.</B><B><A HREF="../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
 258 \r
 259 <BR>\r
 260 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submits job for the execution
 261  Immediate execution is not guaranteed, this method puts the job in the queue.</TD>\r
 262 </TR>\r
 263 </TABLE>\r
 264 &nbsp;\r
 265 <P>\r
 266 <A NAME="compbio.engine.client"><!-- --></A>\r
 267 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 268 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 269 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 270 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
 271 </TR>\r
 272 </TABLE>\r
 273 &nbsp;\r
 274 <P>\r
 275 \r
 276 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 277 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 278 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
 279 </TR>\r
 280 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 281 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 282 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 283 <TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
 284 \r
 285 <BR>\r
 286 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 287 </TR>\r
 288 </TABLE>\r
 289 &nbsp;\r
 290 <P>\r
 291 <A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
 292 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 293 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 294 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 295 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
 296 </TR>\r
 297 </TABLE>\r
 298 &nbsp;\r
 299 <P>\r
 300 \r
 301 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 302 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 303 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
 304 </TR>\r
 305 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 306 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 307 <CODE>&nbsp;void</CODE></FONT></TD>\r
 308 <TD><CODE><B>JobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()">executeJob</A></B>()</CODE>\r
 309 \r
 310 <BR>\r
 311 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 312 </TR>\r
 313 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 314 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 315 <CODE>static&nbsp;<A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A></CODE></FONT></TD>\r
 316 <TD><CODE><B>JobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)">getInstance</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
 317 \r
 318 <BR>\r
 319 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 320 </TR>\r
 321 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 322 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 323 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 324 <TD><CODE><B>AsyncJobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
 325 \r
 326 <BR>\r
 327 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 328 </TR>\r
 329 </TABLE>\r
 330 &nbsp;\r
 331 <P>\r
 332 \r
 333 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 334 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 335 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
 336 </TR>\r
 337 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 338 <TD><CODE><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner(compbio.engine.client.ConfiguredExecutable)">JobRunner</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExec)</CODE>\r
 339 \r
 340 <BR>\r
 341 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 342 </TR>\r
 343 </TABLE>\r
 344 &nbsp;\r
 345 <P>\r
 346 <A NAME="compbio.engine.local"><!-- --></A>\r
 347 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 348 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 349 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 350 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
 351 </TR>\r
 352 </TABLE>\r
 353 &nbsp;\r
 354 <P>\r
 355 \r
 356 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 357 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 358 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
 359 </TR>\r
 360 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 361 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 362 <CODE>&nbsp;void</CODE></FONT></TD>\r
 363 <TD><CODE><B>LocalRunner.</B><B><A HREF="../../../compbio/engine/local/LocalRunner.html#executeJob()">executeJob</A></B>()</CODE>\r
 364 \r
 365 <BR>\r
 366 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 367 </TR>\r
 368 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 369 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 370 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 371 <TD><CODE><B>AsyncLocalRunner.</B><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
 372 \r
 373 <BR>\r
 374 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 375 </TR>\r
 376 </TABLE>\r
 377 &nbsp;\r
 378 <P>\r
 379 \r
 380 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 381 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 382 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
 383 </TR>\r
 384 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 385 <TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)">ExecutableWrapper</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
 386                   java.lang.String&nbsp;workDirectory)</CODE>\r
 387 \r
 388 <BR>\r
 389 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 390 </TR>\r
 391 </TABLE>\r
 392 &nbsp;\r
 393 <P>\r
 394 <A NAME="compbio.metadata"><!-- --></A>\r
 395 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 396 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 397 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 398 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
 399 </TR>\r
 400 </TABLE>\r
 401 &nbsp;\r
 402 <P>\r
 403 \r
 404 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 405 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 406 <TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
 407 </TR>\r
 408 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 409 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 410 <CODE>&nbsp;class</CODE></FONT></TD>\r
 411 <TD><CODE><B><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></B></CODE>\r
 412 \r
 413 <BR>\r
 414 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Thrown if the task larger in size that the limit that applies to the
 415  calculation.</TD>\r
 416 </TR>\r
 417 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 418 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 419 <CODE>&nbsp;class</CODE></FONT></TD>\r
 420 <TD><CODE><B><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></B></CODE>\r
 421 \r
 422 <BR>\r
 423 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Indicates that the server could not execute native executables.</TD>\r
 424 </TR>\r
 425 </TABLE>\r
 426 &nbsp;\r
 427 <P>\r
 428 <A NAME="compbio.ws.server"><!-- --></A>\r
 429 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 430 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 431 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 432 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
 433 </TR>\r
 434 </TABLE>\r
 435 &nbsp;\r
 436 <P>\r
 437 \r
 438 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 439 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 440 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
 441 </TR>\r
 442 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 443 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 444 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 445 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 446 \r
 447 <BR>\r
 448 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 449 </TR>\r
 450 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 451 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 452 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 453 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 454 \r
 455 <BR>\r
 456 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 457 </TR>\r
 458 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 459 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 460 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 461 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 462 \r
 463 <BR>\r
 464 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 465 </TR>\r
 466 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 467 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 468 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 469 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 470 \r
 471 <BR>\r
 472 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 473 </TR>\r
 474 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 475 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 476 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 477 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 478 \r
 479 <BR>\r
 480 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 481 </TR>\r
 482 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 483 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 484 <CODE>static\r
 485 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 486 <TR ALIGN="right" VALIGN="">\r
 487 <TD NOWRAP><FONT SIZE="-1">\r
 488 <CODE>&lt;T&gt; java.lang.String</CODE></FONT></TD>\r
 489 </TR>\r
 490 </TABLE>\r
 491 </CODE></FONT></TD>\r
 492 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 493       <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
 494       org.apache.log4j.Logger&nbsp;statLog,\r
 495       javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
 496       java.lang.String&nbsp;callingMethod,\r
 497       <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
 498 \r
 499 <BR>\r
 500 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 501 </TR>\r
 502 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 503 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 504 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 505 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 506             java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)</CODE>\r
 507 \r
 508 <BR>\r
 509 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 510 </TR>\r
 511 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 512 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 513 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 514 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 515             java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)</CODE>\r
 516 \r
 517 <BR>\r
 518 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 519 </TR>\r
 520 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 521 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 522 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 523 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 524             java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
 525 \r
 526 <BR>\r
 527 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 528 </TR>\r
 529 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 530 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 531 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 532 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 533             java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
 534 \r
 535 <BR>\r
 536 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 537 </TR>\r
 538 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 539 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 540 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 541 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 542             java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)</CODE>\r
 543 \r
 544 <BR>\r
 545 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 546 </TR>\r
 547 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 548 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 549 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 550 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 551             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&nbsp;preset)</CODE>\r
 552 \r
 553 <BR>\r
 554 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 555 </TR>\r
 556 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 557 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 558 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 559 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 560             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&nbsp;preset)</CODE>\r
 561 \r
 562 <BR>\r
 563 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 564 </TR>\r
 565 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 566 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 567 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 568 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 569             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&nbsp;preset)</CODE>\r
 570 \r
 571 <BR>\r
 572 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 573 </TR>\r
 574 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 575 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 576 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 577 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 578             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&nbsp;preset)</CODE>\r
 579 \r
 580 <BR>\r
 581 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 582 </TR>\r
 583 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 584 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 585 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 586 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 587             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&nbsp;preset)</CODE>\r
 588 \r
 589 <BR>\r
 590 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 591 </TR>\r
 592 </TABLE>\r
 593 &nbsp;\r
 594 <P>\r
 595 <HR>\r
 596 \r
 597 \r
 598 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 599 <A NAME="navbar_bottom"><!-- --></A>\r
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